Subsections


dx.map

Image opendx Image grid_search

Synopsis

Create a map of the given space in OpenDX format.

Defaults

dx.map(params=None, map_type=`Iso3D', spin_id=None, inc=20, lower=None, upper=None, axis_incs=5, file_prefix=`map', dir=`dx', point=None, point_file=`point', chi_surface=None, create_par_file=False)

Keyword arguments

params: The parameters to be mapped. This should be an array of strings, the meanings of which are described below.

map_type: The type of map to create. For example the default, a 3D isosurface, the type is `Iso3D'. See below for more details.

spin_id: The spin ID string.

inc: The number of increments to map in each dimension. This value controls the resolution of the map.

lower: The lower bounds of the space. If you wish to change the lower bounds of the map then supply an array of length equal to the number of parameters in the model. A lower bound for each parameter must be supplied. If nothing is supplied then the defaults will be used.

upper: The upper bounds of the space. If you wish to change the upper bounds of the map then supply an array of length equal to the number of parameters in the model. A upper bound for each parameter must be supplied. If nothing is supplied then the defaults will be used.

axis_incs: The number of increments or ticks displaying parameter values along the axes of the OpenDX plot.

file_prefix: The file name. All the output files are prefixed with this name. The main file containing the data points will be called the value of `file'. The OpenDX program will be called `file.net' and the OpenDX import file will be called `file.general'.

dir: The directory to output files to. Set this to `None' if you do not want the files to be placed in subdirectory. If the directory does not exist, it will be created.

point: This argument allows specific points in the optimisation space to be displayed as coloured spheres. This can be used to highlight a minimum or other any other feature of the space. Either a single point or a list of points can be supplied. Each point is a list of floating point numbers in the form [x, y, z]

point_file: The name of that the point output files will be prefixed with.

chi_surface: A list of 4 numbers, setting the level for the 4 isosurfaces. Useful in scripting if you create a set of OpenDX maps with all the same contour levels. Ideal for comparisons.

create_par_file: A flag specifying whether to create a file with parameters and associated chi2 value. The default of False causes the file not to be created.

Description

This will map the space corresponding to the spin identifier and create the OpenDX files. The map type can be changed to one of the following supported map types:

Please see Table 17.2 on page [*].


Table 17.2: OpenDx mapping types.
Surface type Name
3D isosurface 'Iso3D'

Model-free parameters

Please see Table 17.3 on page [*].


Table 17.3: Model-free parameters.
Name Description
tm Global correlation time
Diso Isotropic component of the diffusion tensor
Dx Eigenvalue associated with the x-axis of the diffusion tensor
Dy Eigenvalue associated with the y-axis of the diffusion tensor
Dz Eigenvalue associated with the z-axis of the diffusion tensor
Dpar Diffusion coefficient parallel to the major axis of the spheroid diffusion tensor
Dper Diffusion coefficient perpendicular to the major axis of the spheroid diffusion tensor
Da Anisotropic component of the diffusion tensor
Dr Rhombic component of the diffusion tensor
Dratio Ratio of the parallel and perpendicular components of the spheroid diffusion tensor
alpha The first Euler angle of the ellipsoid diffusion tensor
beta The second Euler angle of the ellipsoid diffusion tensor
gamma The third Euler angle of the ellipsoid diffusion tensor
theta The polar angle defining the major axis of the spheroid diffusion tensor
phi The azimuthal angle defining the major axis of the spheroid diffusion tensor
s2 S2, the model-free generalised order parameter (S2 = S2f.S2s)
s2f S2f, the faster motion model-free generalised order parameter
s2s S2s, the slower motion model-free generalised order parameter
local_tm The spin specific global correlation time (seconds)
te Single motion effective internal correlation time (seconds)
tf Faster motion effective internal correlation time (seconds)
ts Slower motion effective internal correlation time (seconds)
rex Chemical exchange relaxation (sigma_ex = Rex / omega**2)
csa Chemical shift anisotropy (unitless)

N-state model parameters

Please see Table 17.4 on page [*].


Table 17.4: N-state model parameters.
Name Description Type
Axx The Axx component of the alignment tensor float
Ayy The Ayy component of the alignment tensor float
Axy The Axy component of the alignment tensor float
Axz The Axz component of the alignment tensor float
Ayz The Ayz component of the alignment tensor float
probs The probabilities of each state list
alpha The α Euler angles (for the rotation of each state) list
beta The β Euler angles (for the rotation of each state) list
gamma The γ Euler angles (for the rotation of each state) list
paramagnetic_centre The paramagnetic centre list

Relaxation dispersion parameters

Please see Table 17.5 on page [*].


Table 17.5: Relaxation dispersion parameters.
Name Description Type
r2eff The effective transversal relaxation rate dict
i0 The initial intensity dict
r1 The longitudinal relaxation rate dict
r2 The transversal relaxation rate dict
r2a The transversal relaxation rate for state A in the absence of exchange dict
r2b The transversal relaxation rate for state B in the absence of exchange dict
pA The population for state A float
pB The population for state B float
pC The population for state C float
phi_ex The φ_ex = pA.pB.dw**2 value (ppmˆ2) float
phi_ex_B The fast exchange factor between sites A and B (ppmˆ2) float
phi_ex_C The fast exchange factor between sites A and C (ppmˆ2) float
padw2 The pA.dw**2 value (ppmˆ2) float
dw The chemical shift difference between states A and B (in ppm) float
dw_AB The chemical shift difference between states A and B for 3-site exchange (in ppm) float
dw_AC The chemical shift difference between states A and C for 3-site exchange (in ppm) float
dw_BC The chemical shift difference between states B and C for 3-site exchange (in ppm) float
dwH The proton chemical shift difference between states A and B (in ppm) float
dwH_AB The proton chemical shift difference between states A and B for 3-site exchange (in ppm) float
dwH_AC The proton chemical shift difference between states A and C for 3-site exchange (in ppm) float
dwH_BC The proton chemical shift difference between states B and C for 3-site exchange (in ppm) float
kex The exchange rate float
kex_AB The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.sˆ-1) float
kex_AC The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.sˆ-1) float
kex_BC The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.sˆ-1) float
kB Approximate chemical exchange rate constant between sites A and B (rad.sˆ-1) float
kC Approximate chemical exchange rate constant between sites A and C (rad.sˆ-1) float
tex The time of exchange (tex = 1/kex) float
k_AB The exchange rate from state A to state B float
k_BA The exchange rate from state B to state A float

Frame order parameters

Please see Table 17.6 on page [*].


Table 17.6: Frame order parameters.
Name Description
pivot_x The pivot point position x coordinate
pivot_y The pivot point position y coordinate
pivot_z The pivot point position z coordinate
pivot_disp The 2 nd pivot point displacement - the minimum distance between the two rotor axes
ave_pos_x The average position x translation
ave_pos_y The average position y translation
ave_pos_z The average position z translation
ave_pos_alpha The average position α Euler angle
ave_pos_beta The average position β Euler angle
ave_pos_gamma The average position γ Euler angle
eigen_alpha The Eigenframe α Euler angle
eigen_beta The Eigenframe β Euler angle
eigen_gamma The Eigenframe γ Euler angle
axis_theta The cone axis polar angle (for the isotropic cone model)
axis_phi The cone axis azimuthal angle (for the isotropic cone model)
axis_alpha The rotor axis α angle (the rotation angle out of the xy plane)
cone_theta_x The pseudo-ellipse cone opening half-angle for the x-axis
cone_theta_y The pseudo-ellipse cone opening half-angle for the y-axis
cone_theta The isotropic cone opening half-angle
cone_sigma_max The torsion angle
cone_sigma_max_2 The torsion angle of the 2 nd motional mode

Prompt examples

The following commands will generate a map of the extended model-free space for model `m5' consisting of the parameters {S2, S2f, τs}. Files will be output into the directory `dx' and will be prefixed by `map'. In this case, the system is a protein and residue number 6 will be mapped.

[numbers=none]
relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6')

[numbers=none]
relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6', file_prefix='map', dir='dx')

[numbers=none]
relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', inc=20, file_prefix='map', dir='dx')

[numbers=none]
relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', map_type='Iso3D', inc=20, file_prefix='map', dir='dx')

To map the model-free space `m4' for residue 2, spin N6 defined by the parameters {S2, τe, Rex}, name the results `test', and to place the files in the current directory, use one of the following commands:

[numbers=none]
relax> dx.map(['s2', 'te', 'rex'], spin_id=':2@N6', file_prefix='test', dir=None)

[numbers=none]
relax> dx.map(params=['s2', 'te', 'rex'], spin_id=':2@N6', inc=100, file_prefix='test', dir=None)


The relax user manual (PDF), created 2016-10-28.